[Apbs-users] APBS for ligand binding to DNA

[Dayle S. <sm...@wh...>]

Good morning APBS users--
I'm trying to calculate the desolvation free energy for ligand binding 
to DNA, and I have a couple of questions. I'm using APBS from Autodock.  
I have equilibrated structures of DNA+ligand+water+sodium that I have 
calculated using Gromacs, and which will save .pqr files for APBS input.

1) Do I include 22 sodium counterions in the .pqr input file? If not, 
(how) do I account for DNA's 22e charge in APBS?
2) What do I use for the solute dielectric constant?
3) Which quantity in the APBS output is the desolvation free energy?

Thanks a lot,
Dayle Smith
Whitman College